Tuesday, November 29, 2005

Detecting Natural Selection (Part 2)

The Organization of the Genes

This is the third of multiple postings I plan to write about detecting natural selection using molecular data (ie, DNA sequences). The first posting contained a brief introduction and can be found here. The second post described the organization of the genome.

In the last entry I mentioned that the term gene is often used interchangeably with protein coding sequence. In this entry, I will describe the structure of protein coding genes. Only a portion of the gene contains protein coding sequences. We will divide the gene into multiple parts: exons, introns, upstream sequence (or 5’ flanking regions), and downstream sequence (3’ flanking regions). The exons contain the protein coding sequence, and they are separated by introns. The introns and exons are transcribed into RNA, the introns are then spliced out to make messenger RNA (mRNA), and then the mRNA (coding sequence) is translated into a protein.

(Note: The majority of life on earth is prokaryotic, and prokaryotic genes do not contain introns.)

The region upstream of the gene usually contains non-coding sequences that control when and how the coding sequences are transcribed into mRNA (the introns and downstream regions may also contain transcriptional regulatory regions). For more on the regulation of transcription check out this site. For the rest of this discussion, we will refer to two types of sequences: non-coding (introns and upstream and downstream regions) and protein coding.

The protein coding sequence of a gene is made up of sets of three nucleotides called codons. When the mRNA transcribed from a gene is translated into a protein, each codon encodes a single amino acid. Just like nucleotides are the building blocks of DNA, amino acids are the building blocks of proteins. There are 64 different 3 nucleotide combinations (4 different nucleotides in combinations of 3, or 4^3 = 64), but there are only 20 amino acids. That means that some amino acids are encoded by multiple codons. We refer to this as the redundancy of the genetic code.

The U’s in this figure are the RNA equivalent of the T’s in DNA.

The three nucleotides in a codon can each be referred to by their position in the codon: first, second, and third. Because of the redundancy of the genetic code, some codons encode the same amino acid as other codons. The codons that encode the same amino acid tend to have the same first and second nucleotide, but differ at the third codon position. For this reason, many mutations of the third codon position do not lead to a change in the amino acid encoded by the codon.

Mutations that do not lead to a change in the amino acid encoded by a codon are known as synonymous. Conversely, those that lead to a change in amino acid are called non-synonymous. Next time we will discuss how we can compare synonymous and non-synonymous differences between two coding sequences to infer natural selection.

Trudeau on Dilbert

PZ Myers (of Pharyngula) and Scott Adams (creator of Dilbert) had a little disagreement over Adams's credentials to evaluate the biological theory of evolution. I side with PZ on this one -- he is, after all, a trained biologist.

Today, I came across this interview (pdf) with Doonesbury creator Garry Trudeau, in which he discusses the relevancy of his comic, and political cartooning in general, after 35 years of Doonesbury. He talks about satirists finding other outlets (SNL, The Daily Show, Letterman), but also explains his influence in bringing attention to the dialog in cartooning despite mediocre drawing. On this topic, he says:
"[T]he best strip of the last decade is 'Dilbert,' and it sure isn't because of the drawing."
I would say The Boondocks (the strip, not the crappy show on Cartoon Network) and Non-Sequitur have better writing and better drawing than Dilbert. Plus, Non-Sequitur rips on the pseudo-science that Scott Adams is happy to endorse in clever ways that Adams can only aspire to.

Monday, November 28, 2005

My Favorite Obscure Movie

Tony at milkriverblog wants to create a list of bloggers' favorite obscure movies. I was hesitant to get involved because I couldn't think of any. Honestly, I don't really know what my favorite movies are. Then, this post by Sean at Cosmic Variance got me thinking about Terry Gilliam films. Sean watched Brazil recently, which is a good, somewhat obscure Gilliam film -- I like all Gilliam films because of his fearlessness and ability to take risks, even if they end in catastrophe.

So, Tony, I'm going to (belatedly) answer your call for obscure films, limiting myself to only things Gilliam related. I have not chosen a Terry Gilliam film (as they are not very obscure), but rather a film about Terry Gilliam trying to make a film: Lost in La Mancha. This film details the failed attempts of Gilliam and his crew to make The Man Who Killed Don Quixote. If you ever doubted Murphy's Law, this film will make you reconsider your doubts. Basically, everything that can go wrong does.

I would recommend Lost in La Mancha for any Gilliam fan, but I assume that they have all seen it by now. So, I recommend it to anyone who enjoyed Twelve Monkeys, The Adventures of Baron Munchausen (my favorite Gilliam film), Fear and Loathing in Los Vegas, or Time Bandits. It's also a great film for anyone who wants to learn about how movies get made (or not made, for that matter).

Test Your Scientific Literacy

Just to prove that I am qualified to write about the things I write about, I give you this:

You Passed 8th Grade Science

Congratulations, you got 8/8 correct!

Sunday, November 27, 2005

Weekly Random Ten (27 November 2005)

Not So Random Edition

If you came here looking for science, this post will be a disappointment. Sorry. Instead, I'll be talking about something I know very little about: music. It's kind of appropriate given that this is merely an introduction to a (not so) random collection of 10 songs. My taste in music is so bad, I have been told by multiple roommates to stop playing whatever crap I was listening to.

In the spirit of bad taste, I took another one of those stupid online quizzes, and found out which fucked up genius composer I am.

you are Joe Strummer!
Joe Strummer... you've been through the cleansing
fire of punk, only to pick up a few venereal
diseases along the way. You're more of an
optimist when it comes to fucked-up genius.
But you can write wicked-deadly riffs and lyrics.

I thought, "That's cool -- I really like the Clash and the Mescaleros," and it got me to thinking about a documentary that I caught on IFC a short while back, Punk: Attitude. The film is an excellent introduction to early punk from New York City and London, but it falls a bit short when it comes to some of the more recent bands -- and by recent I mean post 1980.

The movie begins with the major influences of early punk: MC5, the Stooges, the New York Dolls from the US, Bowie and Mott the Hoople in the UK. There are other influences (including bands I can't think of off the top of my head and early rock n' roll like Little Richard), but I'm not going to spend all of my time listing them. The film also treats the early days of punk in New York well, showing footage of the Ramones, Richard Hell, the Dictators, and the other CBGBs regulars and interviewing some of the major players in that scene. Of course, the film also deals with the London 1977 scene, including interviews with Paul Simonon, Mick Jones, Poly Styrene, the Slits, Chrissie Hynde, etc.

In all, it's a fun movie for any interested in the history of rock n' roll (especially if you like punk). The old footage of concerts is great, and the folks telling the stories were the machines behind the revolution. The problem comes as the story shifts from the New York and London scene to the bands that were influenced by that music. The New Wave, No Wave, and Synthpop music that followed are briefly mentioned, as are the hardcore bands (they spend some time talking about Agnostic Front, Bad Brains, Black Flag, etc). But almost nothing is said about the California scene -- after a brief mention of Sonic Youth, Fugazi and some other in between bands, the film suddenly jumps to the early 1990s claiming, "Punk disappeared in the 1980s, only to reemerge in Seattle with Nirvana."

The new so-called punk bands (Blink 182, Sum 41) and other rock bands (for some reason, Limp Bizkit gets a fair bit of time in the film -- quite odd), were greatly influenced bands from the 1980s. The music from Los Angeles (Bad Religion, NOFX, Descendents) and the Bay Area (Operation Ivy and the other Gilman Street bands) are the inspiration behind a lot of the stuff that gets called punk today. It's as if the film-makers were trying to fit the film into a neat little 90 minute package, and cut 1985-90 to make it work. Making a documentary on punk and not including Epitaph or Lookout records may not be grounds for exportation from the punk nation, but it's somewhat odd. Also, they briefly mention the dub and reggae that was spun at the London clubs in between sets, but don't really deal with the ska/punk fusion that happened as a result or the two-tone bands that were probably influenced by it (Specials, Madness, etc).

Here it is, a not so random ten consisting of some of my favorite punk songs:
  1. Buzzcocks - Ever Fallen in Love (With Someone You Shouldn't Have Fallen in Love With)?
  2. The Clash - (White Man) in Hammersmith Palais
  3. MC5 - Teenage Lust
  4. Richard Hell and the Voidoids - Blank Generation
  5. Bad Religion - You Are (The Government)
  6. Rancid - Lady Liberty
  7. Operation Ivy - Sound System
  8. Social Distortion - Ball and Chain
  9. Descendents - Jean is Dead
  10. NOFX - Liza and Louise

Saturday, November 26, 2005

Quote of the Day

"If intelligent design really works, then why is my brother so ugly?"
Sam Kwasman, 54, actor, former voice of Donald Duck, Los Angeles

From the New York Times.

Friday, November 25, 2005

Thanksgiving Science Post

A common rumor posits that tryptophan in turkey makes you sleepy after eating your Thanksgiving feast. Afarensis explains why this is erroneous.

Anyone who has taken an introductory genetics course is familiar with the tryptophan operon. This (along with the lac operon) is a classic model of transcriptional/translational regulation in prokaryotes. Operons are the combination of regulatory sequences and coding sequences that allow for expression of genes only when the enzymes encoded by those genes are needed. Otherwise, the genes are not transcribed -- this saves the cell energy because it does not need to create proteins when they are not needed. Transcription and translation are coupled in prokaryotes, so we can essentially use the terms interchangeably.

But what is tryptophan? It is one of the twenty amino acids encoded by the genetic code. It is the largest of the amino acids, and is encoded by a single codon (UGG). Being large means it is expensive to produce, so bacteria regulate its production using an operon, only expressing gene when quantities in the cell are low. Tryptophan is also a precursor for the neurotransmitter serotonin which is important in chemical in mood disorders.

Buy Nothing Day

Traditionally, the day after Thanksgiving in the United States has been known as Black Friday. This marks the first day of the holiday/Christmas shopping season. Retailers offer amazing deals on their products to entice consumers into their stores.

Today (Friday, Nov 25) is also Buy Nothing Day in the United States and Canada, a sort of silent protest against this day of rampant consumerism. I only bring this up because at Thanksgiving dinner yesterday some of my friends were talking about going to Walmart at 5am today to get the best deals. This bothers me on two levels: it gives in to the consumer mentality and it supports a company notorious for its mistreatment of employees.

Happy Buy Nothing Day!

Buy Nothing Day is tomorrow (Saturday, Nov 26) in the U.K.

Thursday, November 24, 2005

I'm Dreaming of . . .

. . . a White Thanksgiving!!

Guess what I was greeted to upon looking out my window this morning.

This is our second snow of the year. We got some in October that melted when it warmed up again. This really throws a wrench in my plans to go for a morning bike ride before gorging myself on Turkey.

Wednesday, November 23, 2005

Detecting Natural Selection (Part 1)

The Organization of the Genome

This is the second of multiple postings I plan to write about detecting natural selection using molecular data (ie, DNA sequences). The first posting contained a brief introduction and can be found here.

Before we can discuss how DNA sequences are used to identify evidence of natural selection, we must have an understanding of how the genome is organized. The genetic material that can be found in each and every one of your cells – and inside every cell in every living organism – is made up of two sugar-phosphate backbones connected by nitrogenous bases. The two strands are wrapped around each other in what is known as a double helix. The nitrogenous bases come in four flavors: adenine (A), guanine (G), thymine (T), and cytosine (C). The nitrogenous base along with the sugar and phosphate is known as a nucleotide. In the double helix, nucleotides pair – A is always paired with T, and G is always paired with C.

One molecule of DNA goes on for millions of nucleotides, and is known as a chromosome. Along with the DNA, chromosomes also have proteins bound to them that help them wrap up into neat little packages. Humans have 46 chromosomes in everyone one of their cells. Each chromosome has a mate, or homolog, that contains nearly all of the same information, so we divide 46 chromosomes into 23 pairs. For each of the 23 pairs, one copy comes from your mother and one from your father. One of these pairs is a special set known as sex chromosomes (ie, X and Y). Females have two copies of the X chromosome (one from their mother and one from their father), whereas males have one X (from mom) and one Y (from dad). The National Center for Biotechnology Information has created a nifty genome browser that lets you explore the contents of each chromosome.

Some of the sequences of nucleotides contain information that leads to the production of proteins. These proteins carry out essential functions within the cell (such as the production of more proteins), allow for communication between cells, and regulate cell division, among the many other tasks they perform. The sequences containing the information to a produce a protein are known as coding sequences. (Note: some people refer to them as genes, but genes may also include sequences that encode RNAs that are never translated into proteins.) Each chromosome contains hundreds of coding sequences interspersed throughout the length of the DNA molecule. In between these coding sequences are non-coding sequences of nucleotides. These non-coding sequences may contain information that determines when and how the coding sequences are translated into proteins.

Here’s a little drawing showing two coding sequences separated by a non-coding sequence.

That’s it for now. Next time we’ll talk about the organization of coding sequences and their regulatory regions. I promise we’ll be discussing natural selection soon.

Tuesday, November 22, 2005

Weekly Random Ten (22 November 2005)

No, this is not a "Special Turkey Day Edition" Edition

I'm sitting here in front of my computer, frustrated by my lack of programming skillz. I'm trying to write a very simple simulation to determine the statistical power of an experiment I performed. Every time I send a variable to a function that does binomial sampling, the variable gets altered. I'm not sending a pointer to the value; I'm sending the actual value. This is really pissing me off. I'm going to move the function into the body of the program and see what happens.

Anyway, that's how my week's been going. Thanksgiving's coming up, and I need to get these simulations done and analyzed, so I can write up the manuscript and submit it for review. I'm hoping to get this all done by the end of the semester, so I can focus my energies on some other analysis next year. We'll see how that goes.

Happy Turkey Day to all my American readers. To all my international readers, have a nice full week of work! I'll be taking some time off to gorge myself on food and watch some football, but nothing can match the excitement of last weekend. Reggie Bush is the second coming (of Gale Sayers), Fresno State is the best two loss team in the nation (yes, better than Notre Dame and Ohio State), and Oregon deserves to go to a BCS bowl game more than any other one loss team (their only loss cam to USC). I guess I just revealed my west-coast bias.

Time to get myself geared up for a tryptophan induced coma -- here's this week's evolgen Random Ten:
  1. Inspector 7 - Sleeping With the Enemy
  2. NOFX - Please Stop Fucking My Mom
  3. Blondie - Maria
  4. Anti-Flag - Die 4 Your Government
  5. Bombshell Rocks - 21st Century Riot
  6. U.S. Bombs - Jaks
  7. 88 Fingers Louie - Go Away
  8. Eric Clapton - Cocaine
  9. Mike Ness - I'm in Love With My Car
  10. Tiger Army - Twenty Flight Rock

Sunday, November 20, 2005

Detecting Natural Selection (Introduction)


This is the first of multiple postings I plan to write about detecting natural selection using molecular data (ie, DNA sequences). A lot of news releases in the popular press recently have dealt with genes under selection in humans. Most people probably don't understand what it means for a gene to be under selection and how researchers detect selection; I often throw around terms like “signature of selection”. These posts will explain some of the basic concepts in molecular evolution and the theory behind how selection is detected. They will be geared toward a scientifically literate reader, and I will do my best to explain the basics of molecular biology and genetics before getting into the nitty gritty. If you can read and understand PZ Myers, you should be in good shape. If John Hawks or Gene Expression are more your taste, this information will probably be old hat.

Throughout these posts, I will address the following:

  1. The organization of the genome
  2. Simple comparative methods for detecting selection
  3. More complex comparative methods
  4. Nucleotide variation in populations
  5. Non-neutral patterns of sequence polymorphism

This is by no means a table of contents, as I have yet to write any of these entries. This will be a sort of dynamic primer of molecular evolution – the next topic will be determined by previous postings.

Check back soon for the first post in this series: “The Organization of the Genome”.

Thursday, November 17, 2005

More Great Fake News

I lamented earlier this week that the fake news does a better job of covering current events than the real news. Here is another example, this time from Sports Pickle:
A major milestone occurred today in the years-old debate over evolution and creation, when a leading creationist admitted he could be convinced that Vikings head coach Mike Tice is descended from apes.

Speaking this morning at a symposium on intelligent design at Princeton, Ken Hammond, who heads the well-known Creation Research Institute, stated that it would not surprise him if Tice's lineage could be traced to apes --– a statement that turns the evolution debate on its ear and likely threatens Hammond'’s standing among creation advocates.

I think they mean Ken Ham, who heads Answers in Genesis, not the Creation Research Institute or the Institute for Creation Research (or the Judean People's Front, for that matter). Maybe they were just watching their asses and didn't want to get sued.

This is especially funny considering the recent goings on surrounding Tice's team, the Minnesota Vikings. You see, some players chartered a couple of boats for a bye week cruise around Lake Minnetonka. The lake itself conjures up images of Purple Rain and Charlie Murphy, but the descriptions of the boat ride (cut short due to improper activity) makes Girls Gone Wild seem tame:
"They were out for a bit, and then the crew was serving drinks and hors d'oeuvres and stuff. I think the first thing they noticed was some of the women that were on board seemed to be either changing clothes or undressing. And then they went into a galley, and there were three of them in the nude that were changing clothes. That was followed by them coming out and some of them doing lap dances.... That's where it started, and then it just progressed to just bizarre."
I'll let you find the details elsewhere (I'm gonna try to keep this site R-rated, and avoid graphic NC-17 stuff). Anyway, Mike Tice is the coach of this team of sexual misfits, who may be charged with violating the Mann Act (transporting a person across state lines for sexual purposes) among other things. Tice, whom I regard as a stellar example of cronyism that causes some sports team to wallow in mediocrity, does look a little bit apish:

To provide support for his hypothesis that Tice descended from apes, "Hammond" presented the following during his talk:
One 20-minute montage of Tice'’s grunting speech patterns --– taken from his post-game press conferences -- were interspersed with monkey noises and left even the most skeptical viewer convinced that current day apes are more evolved than the Vikings coach. But perhaps the most damning evidence was the never-before-seen clip of Tice hurling his feces at former Minnesota receiver Randy Moss. Hammond then concluded his presentation by revealing that the average ape's IQ is 30-percent higher than Tice's.
I'll let them slip with "more evolved" crap, but the image of Tice hurling feces at Randy Moss is even better than Tice tearing a knee ligament while coaching. It would make a great two person Halloween costume: one person dresses up in a gorilla suit and another person wears this mask. Throw in a little novelty fake poo, and you've got the second best Minnesota Vikings themed costume ever.

So, what did we learn today:
  • It's fun to make fun of creationists.
  • It's fun to make fun of sexually adventurous football players.
  • It's fun to make fun of incompetent football coaches.
  • Minnesota is both the home of the purifying waters of Lake Minnetonka and science blogger PZ Myers.

Weekly Random Ten (17 November 2005)

Science Against Evolution Edition

A friend of mine sent me a link to this site -- the official site of Science Against Evolution. I haven't toured the whole place yet, but it seems like an amalgamation of misinformation and common creationist canards.
Science Against Evolution is a California Public Benefit Corporation whose objective is to make the general public aware that the theory of evolution is not consistent with physical evidence and is no longer a respectable theory describing the origin of life.
Ha! Public benefit!? Ask the folks in Dover about the public benefit of violating the establishment clause. Guess what? The theory of evolution does not describe the origin of life, never did describe the origin of life, never will describe the origin of life, and never intends to describe the origin of life. The theory of evolution deals with changes in life on earth since the origin of life -- as Darwin so famously put it, "the origin of species".

They even have an entire page dedicated to "The Failure of Genetics" written in 1998 dealing with this review from Science. If you don't have access, this short review deals with how long external branches and short internal branches lead to incorrect phylogenies when using 18s RNA to determine the relationships of all animals. I'm not as committed to debunking individual creationist lies as some people, and boy is this page loaded with them, but I'll point out a few things.

The article then discusses a figure that shows that mollusks are more closely related to deuterostomes than arthropods when the creatures being compared are a scallop (a mollosk), a sea urchin (a deuterostome), and a brine shrimp (an arthropod). That isn't too surprising. Intuitively, a scallop seems more like a sea urchin than a shrimp, and the 82% correlation between the scallop and sea urchin shown on their diagram isn't surprising.

But when a tarantula is used as the representative of the arthropod, there is a 92% correlation between the scallop and the tarantula. It doesn't seem reasonable that a scallop should be more closely related to a harry [sic], land-dwelling spider than to a sea urchin.

It took me a while to figure out what they mean by "correlation". It turns out that the review has a figure showing bootstrap support of the nodes. Bootstrap values are calculated by randomly sampling the data (with replacement) to come up with a new data set and seeing if the results based on that new data set is consistent with those based on the original data. If you repeat this process multiple times and keep track of how many runs are consistent, you can get the bootstrap support for your data. This has nothing to do with correlation.

And the reason for doing molecular systematics is to overcome our subjective interpretation of phenotypic characters. It doesn't matter what something looks like upon first glance, because convergent evolution can lead to similar appearances despite different origins. You really need to take a much closer look to determine if the characters are homologous. This is so obvious my students look at me like I'm a moron when I tell them it in introductory biology.

If we ignore the author's absolute ignorance regarding simple statistical methods, we can focus on the total misinterpretation of the Science review.
Since the authors are evolutionists, it never occurs to them that the data doesn't agree with the assumed evolutionary relationship because the theory of evolution is wrong. They fall back to the old "evolution happened so fast we must have missed it" argument. They assume a "rapid divergence of most of the animal phyla" that caused not only missing link fossils, but also missing link RNA sequences.
The assumed evolutionary relationship is based on evidence -- assumptions made in scientific models tend to be based on previous studies. The inconsistencies in the trees can be attributed to a describable phenomenon: long branch attraction. If multiple taxa diverge in a short amount of evolutionary time, reassembling the order of divergence will be extremely difficult. This problem can be overcome with better taxanomic sampling. For example, if you add some intermediate relatives for each of the taxa (ie, chordates for the echinoderms), you can remedy the problem of convergent evolution in the rRNA sequences.

Another problem with rRNA is that there is epistatic selection operating to maintain the secondary structure of the molecule so the sights are not independent. To overcome this problem, you can construct trees with amino acid sequences. Ok, I'm sick of this shit . . .

Creationists suck! Here's this week's evolgen Random Ten:
  1. Tiger Army - Outlaw Heart
  2. Jimmy Cliff - Sitting in Limbo
  3. No Use For A Name - On the Outside
  4. Me First and the Gimme Gimmes - It's Raining on Prom Night
  5. Teen Idols - Lovely Day
  6. 311 - What Was I Thinking
  7. Mad Caddies - Booze Cruise
  8. The Von Bondies - Poison Ivy
  9. Redman - I'll Bee Dat!
  10. Hot Hot Heat - Ladies and Gentleman

Tuesday, November 15, 2005

A Barrel of Monkeys

If you don't read The Swift Report, you really should. Here's the headline to a recent article:
Student Suspended Over Evolution Slur
A seventh grade student at a south central Kansas junior high school has been suspended after implying that a classmate was descended from monkeys. School officials say that the student's two-week suspension was merited by the seriousness of the offense.

Classmates say student is member of an outlaw group called the "Biology Club"
The "Biology Club" is known to "typically keep to themselves", be "adherents of the notorious British naturalist Charles Darwin", "wear a lot of black and eat at their own table in the cafeteria." The student was found in possession of the following incriminating drawing:

Liberty Junior High School principal Marty Hamlin says that officials felt that they had no choice but to make an example of DuFresne. "Saying someone is descended from monkeys is about the worst thing you can say about that person. It's as bad as saying that someone's mother is a prostitute, or telling someone that they're adopted when they're not."
I love how the school is called Liberty Junior High, as if it's named after Liberty University, the bastion of science known for hosting the Mega Creation Conference.

As if this isn't enough, check out this article:
God Denies Links to Pat Robertson
God denied having any links to conservative Christian broadcaster Pat Robertson yesterday after He received reports that Mr. Robertson told residents of Dover, P.A., that they had rejected God by voting their school board out of office for supporting "intelligent design" and warned them of His wrath. Sources close to the Higher Being say that He is "tired" of Mr. Robertson and wants him to stop using His name.

God considering filing "cease and desist" letter

Why is it that the fake news seems to cover current events so much better than the real news?

Sunday, November 13, 2005

Browser Switch

I just switched from Netscape 8 to Firefox. I was running Netscape 8 because I liked how it let me view pages using either Firefox or IE, and it has a lot of good features built it (password management, pop up blocking, tabbed browsing, etc). The problem was, it took way too long to load and it kept crashing. I made the switch to Firefox hoping to find the same features (minus the ability to run IE), but I am now going through the process of installing the extensions that give me those features. I have already installed Tab Mixed Plus and JavaScript console. If you use Tab Mixed Plus, how long did it take you to figure out how to configure it properly? Are there any other extensions that are must haves?

As a reward for helping me out, check out this article in press from PNAS:
An index to quantify an individual's scientific research output
J.E. Hirsch
I propose the index h, defined as the number of papers with citation number ≥h, as a useful index to characterize the scientific output of a researcher.
Yes, that's the entire abstract. Hat tip to Richard Gayle. I can't downloaded the PDF from home because my university's library gateway is currently down. If it's interesting, I may comment on it tomorrow when I hook in to the university network.

I need to get back to work shortening a grant proposal to the maximum page length (this has been a procrastination post). I'm caught in a Catch-22 between explaining everything for someone not familiar with bioinformatics and molecular population genetics, not lingering on unnecessary details, and providing enough information for someone who is familiar with the literature in these fields to make an informed evaluation. The entire thing is written, and now I'm selectively pruning.

Saturday, November 12, 2005


You want me update your site?

For those of you that visit this blog regularly, you'll notice some changes to the site. For those of you that read evolgen through an RSS feed, stop by and take a look. I've widened the area allocated for posts so that they aren't forced to fit into narrow text boxes. I also added some blogs to my blogroll (which was in dire need of updating), and deleted some blogs that I either don't read much or aren't very related to the material at my site.

This was just an excuse to post this image:

Political Science

Posted without comment:

Friday, November 11, 2005

Perl of Wisdom

Dinosaur Comics has had guest cartoonist this past week. Today's strip takes a stab at computer science humor.

I was gonna write a joke for you using Perl scripts, but I always have so much trouble with a lot of the Perl expressions. I understand what they are supposed to do, but I can never get the syntax right.

By the way, T-REX is saying "I'm horny" and "booya" in the last panel.

Thursday, November 10, 2005

Weekly Random Ten (10 November 2005)

Just a Theory Edition

Toothpaste for Dinner makes me chuckle again:

Well, after what the creationists have done in Kansas, I say,

"Kansas is just a theory and shouldn't be taught in school."
When kids are required to learn about the fifty states, let's substitute Puerto Rico for Kansas. Kids won't have to learn that Topeka is the capital city of Kansas; instead, they'll be taught about San Juan. Honestly, would you rather learn about a fly over state or a tropical island? The choice is clear, Kansas is just a theory. Come on, do you know of a single person who has ever been to Kansas?

Now that I've pissed off Red State Rabble and Thoughts from Kansas, I give you this week's random ten:

  1. Dropkick Murphys - Do or Die
  2. Goldfinger - My Head
  3. Catch 22 - Walking Away
  4. David Bowie - Ziggy Stardust
  5. Tilt - Pontiac
  6. The Slackers - Wanted Dead or Alive
  7. No Use For A Name - 3 Month Weekend
  8. The Lawrence Arms - 106 South
  9. Tiger Army - Remembered Forever
  10. U.S. Bombs - Lunch in a Sack

Saturday, November 05, 2005

Nature Blogs

Check out the new Nature Genetics blog, Free Association. There aren't any posts there yet, but here's what they say is to come:
Welcome to Free Association, the Nature Genetics blog. Check here regularly for links and editorial comment on research and news in genetics, as well as reader feedback. To contact the editors directly with confidential questions or feedback, please e-mail freeassociation@natureny.com
I found the site through my StatCounter, as they link to my humble blog, along with Pharyngula, The Loom, The Intersection, and other solid science blogs. Does this mean I need to clean this place up and start putting it on my CV?

Friday, November 04, 2005

Weekly Random Ten (4 November 2005)

Them Brotha's Sure Run Fast Edition

When asked why his team lost to TCU the previous Saturday, Air Force football coach Fisher DeBerry replied that TCU "had a lot more Afro-American players than we did and they ran a lot faster than we did . . . It just seems to me to be that way. Afro-American kids can run very well. That doesn't mean that Caucasian kids and other descents can't run, but it's very obvious to me that they run extremely well." DeBerry has since apologized for his statements, saying that he didn't intend to offend anyone (does anyone, really?).

The story doesn't end there, however. DeBerry has a history of -- how can I put this lightly -- offensive tendencies. And, no, these aren't due to the triple option formations that he favors. He recently removed a banner from the locker room advertising "I am a Christian first and last . . . I am a member of Team Jesus Christ" and just scrapped the pregame prayer. DeBerry's first allegiance is to Jesus, and his second is to perpetuating stereotypes. Why not just recruit speed, regardless of race? If you need faster guys to turn the corner on a sweep, move around the end and get outside contain, or track down a speedy return man, then recruit guys with sub 4.4 forty times (sorry if I lost you there with the football jargon). It seems like DeBerry has contracted a case of Paul Hornung syndrome (a recent derivative of Jimmy The Greek condition).

DeBerry isn't the only one coming down with Hornung-itous. Everyone's favorite coke-bottle-glasses wearing football coach, Joe Paterno thinks the brotha's are the reason offensive output (measured in yardage and scoring, not racist statements) has increased in the Big Ten:

"You're looking at kids from Florida, you're looking at kids from Texas, those states. They wouldn't have come to the Big Ten in the old days, probably, if there hadn't been the kind of opportunities we now have because of the practice facilities. You have to be careful the way you say things sometimes. Poor Fisher DeBerry got in trouble, but the black athlete has made a big difference. They have changed the whole tempo of the game. Black athletes have just done a great job as athletes and as people in turning the game around."

JoePa's Nittany Lions are doing well this year (compared to the last couple of seasons of futility) because they've got some solid athletes on offense. Guess where these guys come from: Maryland, Pennsylvania, and Virginia. Not a very long trip from Pennsylvania. Maybe it's due to the recent discovery that there is more to football than three yards and a cloud of dust.

Alright, I'm done playing the race card. Here's this week's Random Ten; my playlist even included one brotha' to increase speed.

  1. Eels - Novacaine for the Soul
  2. The Bouncing Souls - Born to Lose
  3. The Offspring - Jennifer Lost the War
  4. Less Than Jake - My Very Own Flag
  5. Me First and the Gimme Gimmes - Mandy
  6. Mad Caddies - Something's Wrong at the Playground
  7. Ol' Dirty Bastard - Shimmy Shimmy Ya
  8. NOFX - Three on Speed
  9. Living End - Problem
  10. Blink182 - Romeo and Rebecca

Science and Cinema

I'm gonna chime in on this one, even though PZ Myers already has. In case you don't have access, I'm talking about the book review in Nature of Mad, Bad and Dangerous: The Scientist and the Cinema. I haven't read the book, nor do I intend to, so this is neither a review of the book, nor a review of the book review. I have my own little anecdote that I would like to share.

I caught the movie Laurel Canyon on HBO a while back, and I cringed painfully at its portrayal of a graduate student. She was at the thesis writing stage and had moved from Boston to Los Angeles with her fiance (an intern in psychiatry) to live with his mother (a sixties era rock 'n roller in the middle of producing an album for a British pop-rock band). Can't you feel the tension building? A straight-laced doctor and scientist living in a perpetual party atmosphere! I'll pause for a second, and let you wipe the drips of sarcasm from your monitor.

Apparently, the grad student is working in Drosophila genomics, although from the one requisite expository scene you would think she was studying Drah-sew-feel-ee-ah. Honestly, how hard is it to find an expert advisor to ensure the tiny bit of science in the film is presented with a semblance of accuracy? The film takes place less than ten miles from UCLA, a 15-30 minute drive depending on traffic. I’m sure they could have scrounged up a grad student from the molecular biology department to ensure that Drosophila is pronounced correctly. Pay that kid a couple hundred bucks and promise them their name in the credits, and they’ll definitely be in.

From what I remember, the way she describes her project, it sounds like she’s studying protein-protein interactions for the entire proteome, but you can’t be sure. That’s not entirely important, though. What irks me most is that the one time they pay any heed to her research they make her sound like an incompetent moron. In case you’re wondering, she is supposed to be writing her dissertation, but gets caught up in all the sex, drugs and alcohol. Her advisor keeps emailing her, and she keeps ignoring his requests for a completed draft. I would think the guy would have some hook-ups at UCLA, and could set her up with some office space there so that she could get away from the crazy party.

And if you think this is my own little issue that no one else shares, it’s not. I’ve had multiple conversations at Drosophila meetings in which this has come up amongst grad students. We all come to the same conclusion: what the hell is a Drah-sew-feel-ee-ah? It’s not a difficult word to pronounce. Say it with me, “Dro-soph-i-la”.

Wednesday, November 02, 2005

Tangled Bank #40

The Tangled Bank

Tangled Bank #40 is up at the Examining Room of Dr. Charles. Go lern yerself sum cy-ance!